Update ruff and bumpversion configs

CITATION.cff

@@ -27,5 +27,5 @@ doi: "10.5281/zenodo.1090388"
 license: "BSD-3-Clause"
 message: "If you use this software, please cite it using these metadata."
 title: Instamatic
-version: "2.0.1"
+version: "2.0.2"
 ...

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 [project]
 name = "instamatic"
-version = "2.0.1"
+version = "2.0.2"
 description = "Python program for automated electron diffraction data collection"
 readme = "README.md"
 requires-python = ">=3.7"
@@ -125,19 +125,14 @@ target-version = 'py37'
 line-length = 96
 
 [tool.ruff.lint]
-# Enable Pyflakes `E` and `F` codes by default.
 select = [
-	'F',  # Pyflakes
-	'E',  # pycodestyle (error)
-	'W',    # pycodestyle (warning)
-	'I',    # isort
-	'UP',   # pyupgrade
-	'A',    # flake8-builtins
-	'COM',  # flake8-commas
-	'C4',   # flake8-comprehensions
-	'TID',  # flake8-tidy-imports
-    'NPY201',  # numpy deprecation
+    "F",  # Pyflakes
+    "E",  # pycodestyle (error)
+    "W",  # pycodestyle (warning)
+    "I",  # isort
+    "NPY201",  # numpy deprecations
 ]
+
 ignore = [
     'F401',
     'F403',
@@ -148,38 +143,27 @@ ignore = [
     'A003',
 ]
 
+[tool.ruff.lint.isort]
+known-first-party = ['instamatic']
 
-# Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ['A', 'B', 'C', 'D', 'E', 'F', 'I', 'UP', 'BLE', 'COM', 'C4', 'TID',]
-unfixable = []
+[tool.ruff.format]
+quote-style = "single"
+indent-style = "space"
 
-exclude = [
-    '.bzr',
-    '.direnv',
-    '.eggs',
-    '.git',
-    '.hg',
-    '.mypy_cache',
-    '.nox',
-    '.pants.d',
-    '.ruff_cache',
-    '.svn',
-    '.tox',
-    '.venv',
-    '__pypackages__',
-    '_build',
-    'buck-out',
-    'build',
-    'dist',
-    'node_modules',
-    'venv',
-    '.venv',
-    'scripts',
-]
-per-file-ignores = {}
+[tool.bumpversion]
+current_version = "2.0.2"
 
-# Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = '^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$'
+[[tool.bumpversion.files]]
+filename = "src/instamatic/__init__.py"
+search = "__version__ = '{current_version}'"
+replace = "__version__ = '{new_version}'"
 
-[tool.ruff.lint.isort]
-known-first-party = ['instamatic']
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = "version = \"{current_version}\""
+replace = "version = \"{new_version}\""
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+search = "version: {current_version}"
+replace = "version: {new_version}"

src/instamatic/__init__.py

@@ -9,7 +9,7 @@
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 """
 
-__version__ = '2.0.1'
+__version__ = '2.0.2'
 __title__ = 'instamatic'
 __long_title__ = f'{__title__} v{__version__}'
 __author__ = 'Stef Smeets'

src/instamatic/camera/camera_timepix.py

@@ -171,7 +171,7 @@ def read_pixels_cfg(self, filename):
             sys.exit()
 
     def process_real_dac(self, chipnr=None, index=None, key=None, value=None):
-        """int *chipnr."""
+        """Int *chipnr."""
         'int *index'
         'std::string *key'
         'std::string *value'
@@ -237,7 +237,7 @@ def enable_timer(self, enable, us):
         After the Relaxd shutter opens (either explicitly by software or by an
         external trigger), it closes again after the set time.
 
-        bool enable
+        bool enable  
         int us = 10 # microseconds
         """
         enable = c_bool(enable)
@@ -258,7 +258,7 @@ def set_acq_pars(self, pars):
         self.lib.EMCameraObj_setAcqPars(self.obj, byref(pars))
 
     def is_busy(self, busy):
-        """bool *busy."""
+        """Bool *busy."""
         busy = c_bool(busy)
         self.lib.EMCameraObj_isBusy(self.obj, byref(busy))
 

src/instamatic/experiments/autocred/experiment.py

@@ -325,7 +325,8 @@ def img_var(self, img, apert_pos):
             return np.var(img)
 
     def check_img_outsidebeam_byscale(self, img1_scale, img2_scale):
-        """`img1` is the original image for reference, `img2` is the new image."""
+        """`img1` is the original image for reference, `img2` is the new
+        image."""
         if img2_scale / img1_scale < 0.5 or img2_scale / img1_scale > 2:
             return 1
         else:
@@ -595,15 +596,6 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
 
             img0, h = self.defocus_and_image(difffocus=self.diff_defocus, exp_t=self.exposure_time_image)
 
-            """if trackmethod == "p":
-                shift = self.tracking_by_particlerecog(img0)
-                delta_beamshiftcoord = np.matmul(self.calib_beamshift.transform, shift)
-                self.logger.debug("Beam shift coordinates: {}".format(delta_beamshiftcoord))
-
-                bs_x0, bs_y0 = self.setandupdate_bs(bs_x0, bs_y0, delta_beamshiftcoord)
-
-                img0, h = self.defocus_and_image(difffocus = self.diff_defocus, exp_t = self.exposure_time_image)"""
-
             img0_p = preprocess(img0.astype(float))
             scorefromCNN = predict(img0_p)
             # self.print_and_log(logger = self.logger, msg = "Score for the DP: {}".format(scorefromCNN))
@@ -645,8 +637,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
         numb_robustTrack = 0
         """Turn on and off for crystal movement guess here."""
         self.guess_crystmove = False
-
-        """set acquisition time to be around 0.52 s in order to fix the image interval times."""
+        """Set acquisition time to be around 0.52 s in order to fix the image
+        interval times."""
         acquisition_time = self.expt + 0.02
 
         self.ctrl.cam.block()
@@ -665,8 +657,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
                     numb_robustTrack += 1
                 else:
                     self.image_interval = self.nom_ii
-
-                    """If variance changed over 20%, do a robust check to ensure crystal is back"""
+                    """If variance changed over 20%, do a robust check to
+                    ensure crystal is back."""
 
                     if imgvar / img0var < 0.5 or imgvar / img0var > 2 or imgscale / imgscale0 > 1.15 or imgscale / imgscale0 < 0.85:
                         self.image_interval = self.robust_ii
@@ -683,8 +675,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
 
                 if i % self.image_interval == 0:  # aim to make this more dynamically adapted...
                     t_start = time.perf_counter()
-
-                    """Guessing the next particle position by simply apply the same beamshift change as previous"""
+                    """Guessing the next particle position by simply apply the
+                    same beamshift change as previous."""
                     if self.guess_crystmove and i >= self.nom_ii:
                         bs_x0, bs_y0 = self.setandupdate_bs(bs_x0, bs_y0, delta_beamshiftcoord)
 
@@ -701,8 +693,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
                     imgvar = self.img_var(img_cropped, crystal_pos)
 
                     self.logger.debug(f'Image variance: {imgvar}')
-
-                    """If variance changed over 50%, then the crystal is outside the beam and stop data collection"""
+                    """If variance changed over 50%, then the crystal is
+                    outside the beam and stop data collection."""
                     if imgvar / img0var < 0.2 or imgvar / img0var > 5:
                         self.print_and_del('Collection stopping because crystal out of the beam...')
                         self.stopEvent.set()

src/instamatic/server/vm_ubuntu_server.py

@@ -36,11 +36,9 @@ def start_vm_process(vmname=VM_ID, vmachine_pwd=VM_PWD, time_delay=VM_DELAY1, mo
     machine = vbox.find_machine(vmname)
     progress = machine.launch_vm_process(session, mode, '')
     progress.wait_for_completion()
-
-    """wait for certain sec to ensure a normal vm startup"""
+    """Wait for certain sec to ensure a normal vm startup."""
     time.sleep(time_delay)
-
-    """assume vm is password protected"""
+    """Assume vm is password protected."""
     session.console.keyboard.put_keys(vmachine_pwd)
     session.console.keyboard.put_keys(['ENTER'])
     print('password delivered!')
@@ -117,8 +115,8 @@ def vm_ubuntu_start_xds_AtFolder(session, conn, shelxt, unitcell, spgr, composit
 
             session.console.keyboard.put_keys('xds')
             session.console.keyboard.put_keys(['ENTER'])
-
-            """Not sure if I should put some delay here, but just to avoid neglected communication"""
+            """Not sure if I should put some delay here, but just to avoid
+            neglected communication."""
             time.sleep(120)
 
             if shelxt: